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Three episodes into its second season and ABC’s “Marvel’s Agents of S.H.I.E.L.D.” has already covered a lot of ground. They’ve made a home in a new HQ, fought an absorbing man, stolen a Quinjet, infiltrated HYDRA and gotten the Bus back in the air once again. The show has also embarked down some dark paths, an unexpected decision considering how comparatively light-hearted the series was at this time last year. Agent Coulson — now Director Coulson — no longer leads a team of bright-eyed newbies (and Agent May). He has a sniper, a prisoner, a HYDRA mole and a hallucinating lab tech on his team as he desperately tries to rebuild S.H.I.E.L.D. from scratch.

Comic Book Resources sat down with Agent Coulson himself, Clark Gregg, and Jeph Loeb, the head of Marvel TV, during New York Comic Con to discuss “S.H.I.E.L.D.’s” swagger, darkness and dance scenes, along with a look ahead that reveals exactly how the midseason “Agent Carter” series will mirror developments made this season on “Agents of S.H.I.E.L.D.”

CBR News: “Agents of S.H.I.E.L.D.” has come back with a lot of swagger and confidence in Season Two. Does it feel that way on set, coming back for another season?

Jeph Loeb: First we have to give credit where credit is due. Jeff Bell and Jed Whedon and Maurissa Tancharoen, our showrunners; Garry Brown, who’s our producer; Chris Cheramie who runs post; Mark Kolpack, who does the visual effects–

Clark Gregg: The cast.

Loeb: Our incredible cast. You know, these guys just work tirelessly in order to make the best show that we can. The real victory is how invested everybody is in these characters now. And when you think about what we did — at the beginning of last season, it was Clark and here’s five new guys. Hope you like them! And they do. That’s a testament to the writing and the acting and the directing and the emotion of what’s going on. You can’t fake that. Not today. The audience has enough things to watch that they can go, “We’re not going to watch this anymore.” And the fact that they are so invested, and particularly the fans here at New York Comic Con, it’s just the best.

Gregg: I gotta agree. It’s so demanding to try to pull off 22 episodes. There’s a reason not many people are doing it anymore.

Loeb: It’s the best and it’s the worst.

Gregg: Can I be in one of these Netflix shows? Eleven [episodes] sounds so sane.

Loeb: Thirteen, come on!

Gregg: It’s a huge task to maintain a status quo, but one of the thrills of working with Marvel — and certainly with working for Jeph at Marvel TV — is that’s not enough. There’s a responsiveness, there’s a dedication, an overall feeling that you don’t feel at a lot of places. They work for the fans, and the vision comes from here, but there’s a responsiveness there was a refining process that everyone stepped up. The actors stepped up; all of them were kind of given this opportunity. As Jeph said, the way the writers adapted and kind of refined what we were doing and the way the actors rose to the challenge, the way Kolpack just continues to raise the VFX game that the show so depends on, I think is really a testament to how much people care about that.

The group that, really, I think deserves credit is the fans, because, as Jeph said, it’s a world where you’re used to knowing who you’re seeing and, in fact, you read them when you were a kid. Here’s a bunch of new characters that no one knows, and now people really care about Fitz and there’s so much emotion going on. Is he going to come back? That’s because of the great work of Iain De Caestecker and the writers, but the fans really stuck with us and kind of went along realizing it’s really a pretty radical experiment to bring something that’s just barely been possible in the cinematic universe for a couple of years and to try and do that in eight days on television. We’re really grateful for the people that have stuck with us and we’re really glad they’re enjoying it.

Coulson has a very paternal relationship with both Simmons (Elizabeth Henstridge) and Skye (Chloe Bennet), and we’re seeing both of them going down dark paths in these new episodes as Simmons infiltrates HYDRA and Skye turns into a sniper. How does Coulson feel about his surrogate children going down these darker paths?

Gregg: I think all great television shows are about family in one way or another, you know? Everything from “All in the Family” to “The West Wing” — it’s about the working family. That’s what these people are, and these people certainly. That’s something that was really clear about Coulson early in the show, that he never got to have a family. He had this cellist that he knew a little and cared about but didn’t see very often. That’s so lonely. So here are these brilliant, strong, wonderful young women and young men that he has there, and that’s the equivalent of a familial relationship. At the same time, he’s sending his babies undercover into HYDRA. The sleepless worry — the stress factor — is very intense.

Loeb: The idea that Coulson started out as the company man, as somebody who believed in what he was doing, got the order, didn’t question the order, and now he has to be the guy who makes the orders. I think one of the things that’s been really surprising, although we haven’t quite articulated it that way largely because you’re seeing it, is you do now have a better understanding of the difficulty of Fury’s job. That’s the moment I love when you were talking to Fitz in last week’s episode where he said, “Are there things that you’re keeping from me?”

Gregg: “I’m director. There’s a hell of a lot of secrets I’m keeping from you.”

Loeb: That responsibility, it is why the second episode was called “Heavy is the Head.” We are very much exploring that great wish fulfillment; there was a world where Coulson really wanted to be the head of S.H.I.E.L.D. Well, here you go!

Loeb: But having to make those choices. They needed that Quinjet, so that’s the kind of show that it’s become. They are the underdogs, and it was always the challenge from the very beginning. Jeff Bell always likes to talk about, “How do you tell a show where you cheer for the NSA? Yay! They can do anything and no one answers to them!” And now, no one listens to [S.H.I.E.L.D.], and to have Coulson and that team be put under that kind of microscope is both incredible fun and incredibly dangerous.

One of the things we talked about in a post-“Winter Soldier” world, when people found out about Ward [being a traitor], the fun of that was, “Wow, I did not see that coming.” So now what the writers’ room talks about is at the end of every episode, how do we make it so that every week you’re going, “Wow, I didn’t see that coming”? So much as, what the hell is Simmons doing at HYDRA? It’s that kind of thing that you just go, “Okay, I have to come back next week because I do not know what these guys are up to.”

In the next episode we get to see Coulson doing some dancing with Agent May (Ming-Na Wen) as the two of them go undercover. Did you have to go through rigorous training to get those moves down, or were you already a good dancer?

Gregg: I’m not any good at that kind of dancing. [Laughs]

Loeb: Let’s talk a little bit about who you’re married to.

Gregg: I’m married to Jennifer Grey, a wonderful dancer, who won “Dancing with the Stars,” who was in “Dirty Dancing,” and I quickly found that didn’t benefit me at all. [Laughs]

You didn’t just absorb it through osmosis around the house?

Gregg: Honestly, I kinda thought so. I watched “Dancing with the Stars” when she was on it. Why did that mean I couldn’t? There’s episodes that we do that are really — especially this season — that are really dark and terrifying, and there’s ones that have elements of that but also, you know, that’s what I love about Marvel. They don’t shy away from — there’s got to be some moments that are fun and funny and sexy. There’s this terrific relationship between Coulson and his oldest friend, in a way, certainly at S.H.I.E.L.D., in Agent May, played so wonderfully by Ming-Na Wen.

There are people out there who ship, root for the relationship of Coulson and May. They’re called Philinda shippers, [Laughs] and they really get angry if Coulson has flirty [moments with someone besides May]. Poor magnificent Amy Acker comes on to play the cellist and starts getting hate tweets because she’s flirting with Coulson. I knew they would enjoy this [upcoming episode] a lot. I’m excited to see that episode. I love the blend of all the stuff that’s happening this season.

That blend is evident in Coulson’s attitude this season. He is the new director of S.H.I.E.L.D. but every episode still has those moments of Coulson levity that we’ve all come to love. The darkness is there, but there are still moments of light.

Gregg: I care a lot about that, the writers are great about it. It’s always been who Coulson was. I think that’s why people kind of grooved with him early on, because he was able to be a little snarky with Tony Stark even when there was an awful lot on the line. It’s what [“Avengers” director] Joss [Whedon] embraced about him, that tone I think that both [“Iron Man” director] Jon Favreau and [Robert] Downey [Jr.] and everybody at Marvel have found, that even when things get the darkest, people tend to crack wise. That’s Coulson’s world. He loves it there.

Loeb: If there is any Marvel secret sauce, it is always that we want to tell as epic of a story as we can. We do tell stories about aspirational heroes, but there always has to be that levity, there always has to be that secret sauce of humor that is put in there that does make us different from everybody else that works in this [genre]. You have to accept that there is an element of absurdity about what’s going on, that a man can be bombarded by gamma rays and turn into a giant green monster. So unless you can actually comment on that, the audience is commenting. There’s a point in their brains where they’re saying to themselves, “This is ridiculous.”

Gregg: It grounds it. It grounds it, the fact that people are making those jokes in this alternate world is what makes it feel real to me.

With the start of “Agent Carter” coming up later this season, there’s almost a mini-S.H.I.E.L.D. universe within the larger Marvel Cinematic Universe. What relationship will the new show have with “Agents of S.H.I.E.L.D.”?

Loeb: I can’t reveal all of it, and there’s the magical “it’s all connected,” but there was something really fun about being able to sit down at the beginning of the season and say, “Okay, because of what happened last season, Coulson has been tasked with this enormous job of rebuilding S.H.I.E.L.D. What is it, who is it, what are the responsibilities and — most importantly — why is it?” Those are the things that weigh on his character and weigh on the stories that we’re telling. To then be able to go back to 1946 and see Peggy Carter deal with that same issue, which is, should there be — they don’t even have a name for it yet — should there be an organization like this? To see that echo back and forth is tremendously fun and makes “Carter” so relevant now even though it’s a period piece. We don’t want anyone to feel like, “Well, I don’t know what the world was like back in 1946?” You don’t have to care, just come on aboard and watch [“Agent Carter” lead] Hayley Atwell try to figure out the same things that Coulson is trying to figure out in present day — but the world is a different place. So that kind of action, adventure and fun will feel very much like what we refer to as ‘The Mothership,’ but on its own has its own kind of flavor. That’s very much like the movies. Our movies, “Captain America” and “Thor” and “Iron Man,” are all very different films and yet, when you watch them together, it all feels like it’s of a piece. That’s the key to what we’re trying to do.